Plants comprising wheat g-type cytoplasmic male sterility restorer genes, molecular markers and uses thereof

Abstract

Methods are described for selecting or producing a cereal plant comprising a functional restorer gene for wheat G-type cytoplasmic male sterility and nucleic acids for use therein.

1 . A nucleic acid molecule encoding a functional restorer gene allele for wheat G-type cytoplasmic male sterility, wherein said functional restorer gene allele localizes to the scaffold as represented by SEQ ID NO 15. 
     
     
         2 . The nucleic acid molecule of  claim 1 , wherein said functional restorer gene allele is a functional allele of a PPR gene localising to said scaffold. 
     
     
         3 . The nucleic acid of  claim 1  or  2 , wherein said functional restorer gene allele is a functional allele of a PPR gene encoded by SEQ ID NO. 16 or of the polypeptide of SEQ ID NO. 17. 
     
     
         4 . The nucleic acid of any one of  claims 1 - 3 , wherein said functional restorer gene is selected from
 a. A nucleic acid comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO. 16 SEQ ID NO 18, SEQ ID NO: 20, SEQ ID NO. 21, SEQ ID NO. 22;   b. A nucleic acid encoding a polypeptide having at least 85% sequence identity to SEQ ID NO. 17 or 19.   
     
     
         5 . The nucleic acid of any one of  claims 1 - 4 , wherein said functional restorer gene allele has a mutation with respect to SEQ ID NO. 16 that affects mRNA stability or wherein said functional restorer gene allele encodes a PPR protein having a mutation with respect to SEQ ID NO. 17 that affects protein stability or that affects dimerization or that affects hairpin formation between two α-helices making up a PPR motif. 
     
     
         6 . The nucleic acid of any one of  claims 1 - 5 , wherein said functional restorer gene encodes a PPR protein having a mutation in the 13th PPR motif from the C-terminus. 
     
     
         7 . The nucleic acid of any one of  claims 1 - 6 , wherein said functional restorer gene allele encodes a PPR protein capable of binding to the mRNA of ORF256, preferably to nt 139-154 of SEQ ID NO. 24. 
     
     
         8 . The nucleic acid of any one of  claims 1 - 7 , wherein said functional restorer gene allele is obtainable from USDA accession number PI 583676. 
     
     
         9 . The nucleic acid of any one of  claims 1 - 8 , wherein said functional restorer gene allele comprises a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or wherein said functional restorer gene allele encodes a polypeptide comprising an I at the amino acid position corresponding to position 143 of SEQ ID NO. 17. 
     
     
         10 . The nucleic acid of any one of  claims 1 - 9 , wherein said functional restorer gene allele comprises the nucleotide sequence of SEQ ID NO. 18, SEQ ID NO: 20, SEQ ID NO. 21, SEQ ID NO. 22 or encodes the polypeptide of SEQ ID NO. 19. 
     
     
         11 . A polypeptide encoded by the nucleic acid molecule of any one of  claims 1 - 10 . 
     
     
         12 . A chimeric gene comprising the following operably linked elements
 a. a plant-expressible promoter;   b. a nucleic acid comprising the nucleic acid molecule of any one of  claims 1 - 10  or encoding the polypeptide of  claim 11 ; and optionally   c. a transcription termination and polyadenylation region functional in plant cells,   wherein at least one of said operably linked elements is heterologous with respect to at least one other element.   
     
     
         13 . The chimeric gene of  claim 12 , wherein said promoter is capable of directing expression of the operably linked nucleic acid at least during (early) pollen development and meiosis, such as in anther or, more specifically, tapetum, or developing microspores. 
     
     
         14 . A cereal plant cell or cereal plant or seed thereof, such as a wheat plant cell or plant or seed thereof, comprising the nucleic acid molecule of any one of  claims 1 - 10 , polypeptide of  claim 11 , or the chimeric gene of  claim 12  or  13 , wherein said polypeptide, said nucleic acid, or said chimeric gene in each case is heterologous with respect to said plant cell or plant or seed. 
     
     
         15 . A cereal plant, plant part, plant cell or seed, such as wheat, comprising at least one functional restorer gene allele for wheat G-type cytoplasmic male sterility located on chromosome 1B, said plant comprising a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16, said plant not comprising any one or all of: a C at SEQ ID NO: 11; an A at SEQ ID NO: 12, a T at SEQ ID NO: 13; a T at SEQ ID NO: 14. 
     
     
         16 . A method for producing a cereal plant cell or plant or seed thereof, such as a wheat plant cell or plant or seed thereof, comprising a functional restorer gene for wheat G-type cytoplasmic male sterility, or for increasing restoration capacity for wheat G-type cytoplasmic male sterility (“CMS”) in a cereal plant, such as a wheat plant, comprising the steps of providing said plant cell or plant with the nucleic acid molecule of any one of  claims 1 - 10  or the chimeric gene of  claim 12  or  13 , wherein said providing comprises transformation, crossing, backcrossing, genome editing or mutagenesis. 
     
     
         17 . A method for producing a cereal plant cell or plant or seed thereof, such as a wheat plant cell or plant or seed thereof, comprising a functional restorer gene for wheat G-type cytoplasmic male sterility, or for increasing restoration capacity for wheat G-type cytoplasmic male sterility (“CMS”) in a cereal plant, such as a wheat plant, comprising the steps of increasing the expression of a polypeptide according to  claim 11  in said plant cell or plant or seed. 
     
     
         18 . A method for converting a non-restoring cereal plant, such as a wheat plant, into a restoring plant for wheat G-type cytoplasmic male sterility (“CMS”), or for increasing restoration capacity for wheat G-type cytoplasmic male sterility (“CMS”) in a cereal plant, such as a wheat plant, comprising the steps of modifying the genome of said plant to comprise the nucleic acid molecule of any one of  claims 1 - 10  or the chimeric gene of  claim 12  or  13 , wherein said modifying comprises transformation, crossing, backcrossing, genome editing or mutagenesis. 
     
     
         19 . A method for converting a non-restoring cereal plant, such as a wheat plant, into a restoring plant for wheat G-type cytoplasmic male sterility (“CMS”), or for increasing restoration capacity for wheat G-type cytoplasmic male sterility (“CMS”) in a cereal plant, such as a wheat plant, comprising the steps of modifying the genome of said plant to increase the expression of a polypeptide according to  claim 11  in said plant. 
     
     
         20 . A cereal plant cell or cereal plant or seed thereof, such as a wheat plant cell or plant or seed thereof, obtained according to the method of any one of  claims 16 - 19 , preferably wherein said plant has an increased restoration capacity for wheat G-type cytoplasmic male sterility (“CMS”). 
     
     
         21 . The plant cell, plant or seed of  claim 14 ,  15  or  20 , wherein the polypeptide of  claim 8  is expressed at least during (early) pollen development and meiosis, such as in anther or, more specifically, tapetum, or developing microspore. 
     
     
         22 . The plant cell, plant or seed of  claim 14 ,  15 ,  20  or  21 , which is a hybrid plant cell, plant or seed. 
     
     
         23 . A method for selecting a cereal plant comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility or for producing a cereal plant comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility, comprising the steps of:
 (a) Identifying at least one cereal plant comprising at least one marker allele linked to a functional restorer gene allele for wheat G-type cytoplasmic male sterility located on chromosome 1B; and optionally   (b) Selecting the plant comprising said at least one marker allele, wherein said plant comprises said functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B wherein said at least one marker allele is a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or SEQ ID NO. 18.   
     
     
         24 . A method for restoring fertility in a progeny of a G-type cytoplasmic male sterile cereal plant or for producing a fertile progeny plant from a G-type cytoplasmic male sterile cereal parent plant, comprising the steps of:
 (a) Providing a population of progeny plants obtained from crossing a female cereal parent plant with a male cereal parent plant, wherein the female parent plant is a G-type cytoplasmic male sterile cereal plant, and wherein the male parent plant comprises a functional restorer gene allele for wheat G-type cytoplasmic male sterility located on chromosome 1B;   (b) Identifying in said population a fertile progeny plant comprising at least one marker allele linked to said functional restorer gene allele for wheat G-type cytoplasmic male sterility, wherein said progeny plant comprises said functional restorer gene allele for wheat G-type cytoplasmic male sterility located on chromosome 1B; and optionally   (c) Selecting said fertile progeny plant; and optionally   (d) Propagating the fertile progeny plant,   
       wherein said at least one marker allele is a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or SEQ ID NO. 18. 
     
     
         25 . The method of  claims 23  or  24 , wherein said functional restorer gene allele comprises a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or wherein said functional restorer gene allele comprises an I at the amino acid position corresponding to position 143 of SEQ ID NO. 17. 
     
     
         26 . The method of any one of  claims 23 - 25 , wherein said functional restorer gene allele comprises the nucleotide sequence of SEQ ID NO. 18, SEQ ID NO. 20 or SEQ ID NO. 21 or SEQ ID NO. 22 or encodes the polypeptide of SEQ ID NO. 19 
     
     
         27 . A method for identifying and/or selecting a cereal (e.g. wheat) plant comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility comprising the steps of
 a. Identifying or detecting in said plant the presence of a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or SEQ ID NO. 18; and optionally   b. selecting said plant having a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or SEQ ID NO. 18.   
     
     
         28 . A method for identifying and/or selecting a cereal (e.g. wheat) plant comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility comprising the steps of
 a. Identifying or detecting in said plant the presence of a nucleic acid of any one of  claims 1 - 10  or of the polypeptide according to  claim 11 , or the chimeric gene of  claim 12  or  13 .   b. and optionally selecting said plant comprising said nucleic acid or polypeptide or chimeric gene.   
     
     
         29 . The method of  claim 28 , wherein said polypeptide is expressed at least during (early) pollen development and meiosis, such as in anther or, more specifically, tapetum, or developing microspore. 
     
     
         30 . A method for producing a cereal plant, such as a wheat plant, comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility, comprising the steps of
 a. crossing a first cereal plant, such as a wheat plant, comprising a functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B as described in any one of  claims 23 - 26  or a plant of any one of  claims 14 ,  15 ,  20  or  21  with a second cereal plant   b. identifying a progeny plant comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility according to the method of any one of  claims 23 - 26  or  27 - 29 .   
     
     
         31 . A method for producing a cereal plant, such as a wheat plant, comprising a functional restorer gene allele for wheat G-type cytoplasmic male sterility, comprising the steps of
 a. crossing a first cereal plant, such as a wheat plant, homozygous for a functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B as described in any one of  claims 23 - 26  or a plant of any one of  claims 14 ,  15 ,  20  or  21 , with a second cereal plant   b. obtaining a progeny plant, wherein said progeny plant comprises a functional restorer gene allele for wheat G-type cytoplasmic male sterility.   
     
     
         32 . A method for producing hybrid seed, comprising the steps of:
 a. Providing a male cereal parent plant, such as a wheat plant, comprising at least one marker allele linked to a functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B as described in any one of  claims 23 - 26 , said male parent plant comprising said functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B as described in any one of  claims 23 - 26 , or providing a male cereal parent plant according to  claim 14 ,  15 ,  20  or  21 , said plant comprising said functional restorer gene allele for wheat G-type cytoplasmic male sterility, wherein said functional restorer gene allele is preferably present in homozygous form.   b. Providing a female cereal parent plant that is a G-type cytoplasmic male sterile cereal plant.   c. Crossing said female cereal parent plant with a said male cereal parent plant; and optionally   d. Harvesting seeds.   
     
     
         33 . The method of any one of  claims 30 - 32 , wherein said first plant or said male parent plant has been selected according to the method of any one of  claims 23 - 26 . 
     
     
         34 . A method for determining the presence or absence or zygosity status of a functional restorer gene allele for wheat G-type cytoplasmic male sterility located on chromosome 1B in a biological sample, comprising the steps of
 a. providing genomic DNA from said biological sample, and   b. analysing said DNA for the presence or absence or zygosity status of at least one marker allele linked to said functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B   wherein said at least one marker allele is a C at the nucleotide position corresponding to nucleotide position 429 of SEQ ID NO 16 or SEQ ID NO. 18.   
     
     
         35 . Use of the nucleic acid of any one of  claims 1 - 10  to identify one or more further functional restorer gene alleles for wheat G-type cytoplasmic male sterility. 
     
     
         36 . Use of at least one marker comprising an allele linked to a functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B as described in any one of  claims 23 - 26  to identify at least one further marker comprising an allele linked to a functional restorer gene for wheat G-type cytoplasmic male sterility located on chromosome 1B. 
     
     
         37 . Use of at least one marker comprising an allele linked to a functional restorer gene allele for wheat G-type cytoplasmic male sterility located on chromosome 1B as described in any one of  claims 23 - 26  or of the nucleic acid of any one of  claims 1 - 10  of the polypeptide according to  claim 11  or the chimeric gene of  claim 12  or  13  for the identification of a plant comprising said functional restorer gene allele for wheat G-type cytoplasmic male sterility. 
     
     
         38 . Use of a plant of any one of  claims 14 ,  15 ,  20  or  21  or a plant obtained by the method of any one of  claims 16 - 19  or  30 - 33 , said plant comprising said functional restorer gene for wheat G-type cytoplasmic male sterility, for restoring fertility in a progeny of a G-type cytoplasmic male sterile cereal plant, such as a wheat plant. 
     
     
         39 . Use of a plant of any one of  claims 14 ,  15 ,  20  or  21  or a plant obtained by any one of  claims 16 - 19  or  30 - 33 , said plant comprising said functional restorer gene for wheat G-type cytoplasmic male sterility, for producing hybrid seed or a population of hybrid cereal plants, such as wheat seed or plants.